EP3766580B1 - Microfluidic device for preparing and analysing a biological sample - Google Patents

Description

Technical field of the invention

The present invention relates to a microfluidic device for preparing and analyzing a biological sample containing biological species.

This device makes it possible in particular to carry out all the stages of preparation and analysis of the sample in the same rigid support.

State of the art

Since the invention of PCR (“Polymerase Chain Reaction”) and even of qPCR (“Quantitative PCR”), numerous applications have been developed around molecular biology to detect and identify organisms from their nucleic acids. In most cases, this involves detection by PCR using DNA primers specific to a given target (rare cells in the blood, viruses in the respiratory tract or bacteria in food matrices). A preamplification step by culture of the cells sought is often necessary because the test is not always sensitive enough to detect very low concentrations or the matrix and the cell (or bacterial, or viral) lysis reagent in which the sample inhibits the test (eg blood, cheese, etc.). It is then necessary to dilute the sample to decrease the inhibitors, which leads to a dilution of the target cells or DNA.

Currently, the known tests are carried out in three main phases: a phase of culturing the sample, then lysis of the cells to make the DNA accessible, then a phase of purification or dilution of the nucleic acids present and of biomolecular amplification. . The cultivation phase is inexpensive but turns out to be very long (from 8h to 72h). The phase of DNA release and purification / dilution for the amplification of nucleic acids requires for its part many manipulations, which makes it difficult to understand by unqualified personnel. It can certainly be carried out automatically, but the known devices are often large and expensive.

• enrichissement dans un milieu de culture,
• concentration des espèces biologiques présentes dans l'échantillon,
• purification des espèces biologiques ciblées,
• lyse des espèces biologiques contenues dans l'échantillon pour casser lesdites espèces et libérer un matériel biologique à analyser,
• purification et ou dilution du matériel biologique,
• amplification biomoléculaire de type qPCR, LAMP, RPA, ou tout autre mode de détection par amplification biomoléculaire ou séquençage
• détection de l'amplification à chaque cycle par optique tel que par exemple fluorescence, colorimétrie, imagerie holographique, turbidimétrie, pHmétrie en liaison avec la réaction d'amplification.

The detection of pathogens in a biological sample is therefore often carried out in the laboratory by using heavy equipment that is poorly suited to rapid analysis in the field. As a reminder, setting up such a detection on a biological sample may require performing all of the following steps:

• enrichment in a culture medium,
• concentration of biological species present in the sample,
• purification of targeted biological species,
• lysis of the biological species contained in the sample to break said species and release a biological material to be analyzed,
• purification and or dilution of biological material,
• biomolecular amplification of the qPCR, LAMP, RPA type, or any other method of detection by biomolecular amplification or sequencing
• detection of the amplification at each cycle by optics such as for example fluorescence, colorimetry, holographic imaging, turbidimetry, pHmetry in connection with the amplification reaction.

Devices which make it possible to implement some of the steps described above, in particular the steps of concentration, purification and mechanical lysis, are known from the state of the art. The demand for patent WO2015 / 181743A1 describes in particular such a device. In this, the mechanical lysis is carried out by shearing between two walls, one of the two walls having a rough bearing surface. Such a device essentially makes it possible to carry out the grinding and is not suitable for carrying out a more complete analysis of a biological sample, the analysis by optical detection having to be carried out after transfer of the sample outside the device, this which can lead to sample contamination and false results.

• « Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes », Nathan A. Tanner et al - BioTechniques, Vol. 58, n°2, February 2015, pp. 59-68 .
• « Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue », Motoki Goto et al. - BioTechniques, Vol. 46, No. 3, March 2009, pp. 167-172 .
• « Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains of Escherichia coli », Hill J, Beriwal S, Chandra I, et al. - Journal of Clinical Microbiology. 2008;46(8):2800-2804. doi:10.1128/JCM.00152-08 .
• « Visual Detection of Norovirus Genogroup II by Reverse Transcription Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye », Jianming, Ziqian Xu, Kai Nie, Xiong Ding, Li Guan, Ji Wang, Yuying Xian, Xiyang Wu , Xuejun Ma - Food and Environmental Virology, September 2014, Volume 6, Issue 3, pp 196-201 .

There are also solutions which make it possible to detect the presence of pathogens by amplification and detection by colorimetry or turbidity. Such solutions are for example described in the following publications:

• “Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes”, Nathan A. Tanner et al - BioTechniques, Vol. 58, n ° 2, February 2015, pp. 59-68 .
• “Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue”, Motoki Goto et al. - BioTechniques, Vol. 46, No. 3, March 2009, pp. 167-172 .
• “Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Common Strains of Escherichia coli”, Hill J, Beriwal S, Chandra I, et al. - Journal of Clinical Microbiology. 2008; 46 (8): 2800-2804. doi: 10.1128 / JCM.00152-08 .
• "Visual Detection of Norovirus Genogroup II by Reverse Transcription Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye", Jianming, Ziqian Xu, Kai Nie, Xiong Ding, Li Guan, Ji Wang, Yuying Xian, Xiyang Wu, Xuejun Ma - Food and Environmental Virology, September 2014, Volume 6, Issue 3, pp 196-201 .

The document US 2002/124896 A1 describes modular microfluidic systems optionally including a filtration module. The document US 2016/077062 A1 relates to a microfluidic injection device implementing the insertion of an element. The patent EP3222989B1 describes for its part a microfluidic device which also makes it possible to carry out some of the steps described above, in particular the concentration, lysis and detection by optical reading.

This latter device is therefore particularly complete, but it does not make it possible to implement all the steps described above. Moreover, even if certain steps may remain optional, it is useful to have a more versatile device which makes it possible to carry out all the steps without transferring the sample outside the device and therefore without risk of contamination.

Disclosure of the invention

• Un unique support rigide,
• Une première unité comprenant une première chambre de volume non nul délimitée par des parois du support, un filtre séparant ladite première chambre en un premier espace et un deuxième espace, un premier canal réalisé dans ledit support débouchant à une extrémité sur une surface dudit support et à une autre extrémité dans ledit premier espace et un deuxième canal réalisé dans ledit support et débouchant à une extrémité sur une surface dudit support et à une autre extrémité dans ledit deuxième espace,
• Une deuxième unité comprenant une deuxième chambre réalisée dans ledit support rigide et délimitée au moins partiellement par une paroi transparente dudit support, un troisième canal réalisé dans ledit support et débouchant à une extrémité sur une surface dudit support et à une autre extrémité dans ladite deuxième chambre,
• Un premier canal de transfert fluidique entre la première chambre et la deuxième chambre, réalisé dans ledit support et débouchant d'une part dans ladite deuxième chambre et d'autre part en un premier nœud de dérivation dans ledit deuxième canal,
• Des premiers moyens d'aiguillage de flux agencés pour sélectionner la liaison de la première chambre :
  • ∘ vers l'extérieur uniquement via le deuxième canal uniquement ou,
  • ∘ vers la deuxième chambre uniquement à travers le premier canal de transfert.

This versatile microfluidic device thus allows the preparation and analysis of a biological sample and comprises:

• A single rigid support,
• A first unit comprising a first chamber of non-zero volume delimited by the walls of the support, a filter separating said first chamber into a first space and a second space, a first channel formed in said support opening at one end onto a surface of said support and at another end in said first space and a second channel formed in said support and opening at one end onto a surface of said support and at another end into said second space,
• A second unit comprising a second chamber made in said rigid support and delimited at least partially by a transparent wall of said support, a third channel made in said support and opening at one end on a surface of said support and at another end in said second chamber ,
• A first fluidic transfer channel between the first chamber and the second chamber, produced in said support and opening out on the one hand into said second chamber and on the other hand into a first bypass node in said second channel,
• First flow routing means arranged to select the connection of the first chamber:
  • ∘ to the outside only via the second channel only or,
  • ∘ to the second chamber only through the first transfer channel.

According to one feature, the first unit comprises a rough bearing surface produced at the bottom of its first chamber.

According to another feature, the first chamber is closed by a deformable membrane.

• Concentration des espèces biologiques présentes dans un échantillon biologique,
• Lavage pour purification des espèces biologiques,
• Réception d'un milieu de culture,
• Culture des espèces biologiques,
• Lyse des espèces biologiques en vue de libérer un matériel biologique,
• Séparation du matériel biologique.

According to another feature, the first unit is configured to implement one or more of the following steps of a method for preparing and analyzing a biological sample:

• Concentration of biological species present in a biological sample,
• Washing for purification of biological species,
• Reception of a culture medium,
• Cultivation of organic species,
• Lysis of biological species in order to release biological material,
• Separation of biological material.

• Culture des espèces biologiques,
• Suivi optique de croissance lors de ladite étape de culture,
• Détection de présence de pathogènes dans le matériel biologique séparé, par amplification biomoléculaire.

According to another feature, the second unit is configured to implement one or more of the following steps of a method for preparing and analyzing a biological sample:

• Cultivation of organic species,
• Optical growth monitoring during said culture step,
• Detection of the presence of pathogens in the separated biological material, by biomolecular amplification.

According to another feature, the device comprises a first hydrophobic membrane closing off the third channel.

• Une troisième unité comprenant une troisième chambre réalisée dans ledit support rigide et délimitée au moins partiellement par une paroi transparente dudit support, un quatrième canal réalisé dans ledit support et débouchant à une extrémité sur une surface dudit support et à une autre extrémité dans ladite troisième chambre.

According to another feature, the device comprises:

• A third unit comprising a third chamber made in said rigid support and delimited at least partially by a transparent wall of said support, a fourth channel made in said support and opening at one end onto a surface of said support and at another end into said third chamber .

• Un deuxième canal de transfert fluidique entre la première chambre (10) et la troisième chambre, réalisé dans ledit support et débouchant d'une part dans ladite troisième chambre et d'autre part en un deuxième nœud de dérivation dans ledit premier canal.

According to another feature, the device comprises:

• A second fluidic transfer channel between the first chamber (10) and the third chamber, produced in said support and opening out on the one hand in said third chamber and on the other hand in a second bypass node in said first channel.

• vers l'extérieur uniquement via le premier canal uniquement ou,
• vers la troisième chambre uniquement à travers le deuxième canal de transfert.

According to another feature, the device comprises second flow routing means arranged to select the connection of the first chamber:

• to the outside only via the first channel only or,
• to the third chamber only through the second transfer channel.

• Détection de présence de pathogènes dans le matériel biologique séparé, par amplification biomoléculaire.

According to another feature, the third unit is configured to implement the following step of a method for preparing and analyzing a biological sample:

• Detection of the presence of pathogens in the separated biological material, by biomolecular amplification.

According to another particularity, the device comprises a second hydrophobic membrane closing off the fourth channel.

The qPCR-type reaction consists of an amplification of a targeted DNA or RNA sequence (representative of a particular organism) coupled to an intercalator or a probe producing a fluorescence detectable by an optical device in the event of amplification. of this sequence. Thus, if the level of fluorescence increases during the reaction, it means that the amplification reaction is occurring and that therefore the DNA or RNA of the target organism was indeed present. However, if there is no reaction, you must be able to say that this is due to the absence of the desired organism and not to an inhibition of the amplification reaction, which would give rise to a false negative. . The enzymes responsible for the amplification reaction are in fact sensitive to many inhibitors provided by the sample analyzed.

• L'une d'elles pourrait être d'utiliser une partie de l'échantillon pour réaliser le contrôle en parallèle, en tant que réaction indépendante. Ceci oblige à fractionner l'échantillon initial entrainant une perte de la sensibilité/représentativité du test. L'avantage est qu'il est possible d'utiliser n'importe quelle technique de détection d'amplification pour ce contrôle (exemple : intercalant ADN fluorescent).
• Afin de ne pas diviser l'échantillon, une autre stratégie consiste à réaliser le contrôle dans la même réaction que la séquence ciblée : avec par exemple l'utilisation de sondes ADN spécifiques de la séquence cible et en parallèle des sondes ADN spécifiques de la séquence contrôle (avec un fluorochrome différent pour chaque sonde). Cette solution permet de tester l'intégralité de l'échantillon mais n'est pas compatible avec toutes les techniques de détection, notamment avec l'utilisation d'agent intercalent non spécifique, d'une séquence ou de tout autre mode de détection non spécifique de séquence (colorimetrie, pH metrie..).

In order to ensure that the absence of amplification means the absence of the target, internal reaction controls are put in place. Most of the time, this is another DNA target added on purpose to the test that will be amplified simultaneously with the sample of interest. We must then be able to discriminate between the two reactions. Several strategies are used in the industry:

• One of these could be to use part of the sample to run the control in parallel, as an independent reaction. This makes it necessary to split the initial sample leading to a loss of the sensitivity / representativeness of the test. The advantage is that it is possible to use any amplification detection technique for this control (example: fluorescent DNA intercalator).
• In order not to divide the sample, another strategy consists in carrying out the control in the same reaction as the targeted sequence: for example with the use of DNA probes specific for the target sequence and in parallel DNA probes specific for the sequence. control (with a different fluorochrome for each probe). This solution makes it possible to test the entire sample but is not compatible with all detection techniques, in particular with the use of a non-specific intercalating agent, of a sequence or of any other non-specific detection method. sequence (colorimetry, pH metry ..).

The patent application EP0586112A2 and the patent US6312930B1 each describe a detection method making it possible to eliminate false negatives by adding a control target.

The invention therefore also aims to give the second chamber a particular architecture, by shaping its internal volume.

According to another feature, the second chamber thus comprises at least one alcove intended to receive an internal reaction control compound.

According to another feature, the second chamber is made in several superimposed layers and in that said alcove is made in one of said layers only.

• La première unité est configurée pour mettre en œuvre une ou plusieurs des étapes suivantes dudit procédé :
  • ∘ Concentration des espèces biologiques présentes dans un échantillon biologique,
  • ∘ Lavage pour purification des espèces biologiques,
  • ∘ Réception d'un milieu de culture,
  • ∘ Culture des espèces biologiques,
  • ∘ Lyse des espèces biologiques en vue de libérer un matériel biologique,
  • ∘ Séparation du matériel biologique,
• La deuxième unité est configurée pour mettre en œuvre une ou plusieurs des étapes suivantes dudit procédé :
  • ∘ Culture des espèces biologiques,
  • ∘ Suivi optique de croissance lors de ladite étape de culture,
  • ∘ Détection de présence de pathogènes dans le matériel biologique séparé, par amplification biomoléculaire,
• La troisième unité est configurée pour mettre en œuvre l'étape suivante dudit procédé :
  • ∘ Détection de présence de pathogènes dans le matériel biologique séparé, par amplification biomoléculaire.

The invention also relates to a method for preparing and analyzing a biological sample containing biological species, said method being implemented using a microfluidic device as defined above, in which:

• The first unit is configured to implement one or more of the following steps of said method:
  • ∘ Concentration of biological species present in a biological sample,
  • ∘ Washing for purification of biological species,
  • ∘ Reception of a culture medium,
  • ∘ Cultivation of organic species,
  • ∘ Lysis of biological species in order to release biological material,
  • ∘ Separation of biological material,
• The second unit is configured to implement one or more of the following steps of said method:
  • ∘ Cultivation of organic species,
  • ∘ Optical growth monitoring during said culture step,
  • ∘ Detection of the presence of pathogens in the separated biological material, by biomolecular amplification,
• The third unit is configured to implement the following step of said method:
  • ∘ Detection of the presence of pathogens in the separated biological material, by biomolecular amplification.

Brief description of the figures

• La figure 1 illustre les différentes configurations possibles d'un procédé de préparation et d'analyse d'un échantillon contenant des espèces biologiques.
• Les figures 2A à 2C représentent trois variantes de réalisation du dispositif de l'invention.
• Les figures 3A à 3D représentent les différentes étapes de préparation et d'analyse mises en œuvre avec le dispositif de la figure 2A.
• Les figures 4A à 4H représentent les différentes étapes de préparation et d'analyse mises en œuvre avec le dispositif de la figure 2B.
• Les figures 5A à 5F représentent les différentes étapes de préparation et d'analyse mises en œuvre avec le dispositif de la figure 2C.
• La figure 6 représente, vu en éclaté, un exemple de réalisation du dispositif de l'invention, dans la variante de la figure 2B.
• La figure 7 représente un exemple d'une chambre d'amplification pouvant être employée dans le dispositif de l'invention.
• Les figures 8A à 8C représentent plusieurs variantes de réalisation de la strate inférieure de la chambre d'amplification, pouvant être employée dans le dispositif de l'invention.

Other characteristics and advantages will appear in the detailed description which follows given with reference to the appended drawings in which:

• The figure 1 illustrates the different possible configurations of a method for preparing and analyzing a sample containing biological species.
• The figures 2A to 2C represent three variant embodiments of the device of the invention.
• The figures 3A to 3D represent the different stages of preparation and analysis implemented with the system of the figure 2A .
• The figures 4A to 4H represent the different stages of preparation and analysis implemented with the system of the figure 2B .
• The figures 5A to 5F represent the different stages of preparation and analysis implemented with the system of the figure 2C .
• The figure 6 shows, exploded view, an exemplary embodiment of the device of the invention, in the variant of the figure 2B .
• The figure 7 shows an example of an amplification chamber that can be used in the device of the invention.
• The figures 8A to 8C represent several variant embodiments of the lower stratum of the amplification chamber, which can be used in the device of the invention.

Detailed description of at least one embodiment

The microfluidic device of the invention is intended for the analysis of a biological sample. This biological sample is for example in the form of a fluid which contains biological species containing biological material to be studied.

The term “biological species” is understood to mean in particular microorganisms, cells, spores, viruses, etc. proteins, lipopolysaccharides (LPS), lipoteichoic acids (LTA) ...

The term “fluid” is understood to mean in particular a liquid, a gas, etc. The liquid may have different degrees of viscosity and may for example be in the form of a paste or a gel.

In the remainder of the description, the terms “lower”, “upper”, “top” and “bottom” used are to be understood by taking as reference a main axis (X) which is vertical.

In the remainder of the description, the terms “external”, “exterior”, “internal”, “interior” must be understood by taking as a reference the chambers of the device which will be described below.

• E1 : Concentration des espèces biologiques présentes dans l'échantillon biologique,
• E2 : Lavage pour purification, pour élimination des interférents de culture,
• E3 : Apport d'un milieu de culture,
• E4 : Culture des espèces biologiques,
• E5 : Suivi optique de croissance lors de la culture et comptage des colonies,
• E6 : Lavage, pour élimination des inhibiteurs de PCR,
• E7 : Lyse mécanique des espèces biologiques présentes dans l'échantillon en vue d'en extraire un matériel biologique à étudier,
• E8 : Séparation entre le matériel biologique à étudier et les polluants présents,
• E9 : Une détection de présence de pathogènes dans le matériel biologique par amplification biomoléculaire de type qPCR, LAMP, RPA et détection optique tel que par exemple fluorescence, colorimétrie, imagerie holographique, turbidimétrie, pHmétrie en liaison avec la réaction d'amplification.

With reference to the figure 1 , the complete analysis (column C0) of a biological sample may include the following steps carried out successively:

• E1: Concentration of biological species present in the biological sample,
• E2: Washing for purification, for elimination of culture interferences,
• E3: Contribution of a culture medium,
• E4: Culture of organic species,
• E5: Optical growth monitoring during culture and counting of colonies,
• E6: Washing, to remove PCR inhibitors,
• E7: Mechanical lysis of the biological species present in the sample with a view to extracting therefrom a biological material to be studied,
• E8: Separation between the biological material to be studied and the pollutants present,
• E9: Detection of the presence of pathogens in biological material by biomolecular amplification of the qPCR, LAMP, RPA type and optical detection such as for example fluorescence, colorimetry, holographic imaging, turbidimetry, pHmetry in connection with the amplification reaction.

During the concentration step, the biological sample, for example in liquid form, comprising the biological species, is injected into a chamber to pass through a filter. The liquid part of the sample and any particles / molecules which pass through the filter are collected by an evacuation channel and removed from the analysis. The biological species are then concentrated in a space of the chamber.

A wash / rinse solution can be injected to wash the biological species present in the chamber.

A culture medium is injected to allow the culture of the biological species.

The growth monitoring step makes it possible, by optical reading, to monitor cell growth during the culture step.

Mechanical lysis of biological species is implemented to crush the biological species present in the sample against a rough bearing surface. Once the mechanical lysis has been carried out, there is a biological material to study, formed for example of DNA molecules and pollutants.

The separation between the biological material to be studied and the pollutants is carried out by injecting a liquid solution containing amplification reagents, to elute the biological material to be studied. Part of the injected liquid solution thus carries away the biological material to be studied, for example DNA molecules, which passes through the filter.

Once the separation between the pollutants and the biological material to be studied is carried out, the amplification reaction of the biological material makes it possible to detect the presence of a pathogen in the biological material which has been separated. The amplification reaction is carried out by adding an amplification mixture and heating a chamber in which the sample is placed. The temperature to which the chamber is heated depends on the type of amplification reaction implemented. He will be able to it involves all types of amplification reactions, for example LAMP ("Loop-Mediated Isothermal Amplification"), PCR ("Polymerase Chain Reaction"), NASBA ("Nucleic Acid Sequence Based Amplification"), RPA ("Recombinase Polymerase Amplification ") ... For an amplification of the LAMP type, the heating is carried out at a temperature advantageously between 60 ° C and 65 ° C. This reaction makes it possible to amplify the molecules of the biological material to be detected, for example DNA molecules. During the amplification reaction of biological material, it is a question of detecting whether a pathogen is present. For this, it is possible to use different methods, such as for example colorimetry, fluorescence, electrochemistry, pHmetry, turbidity measurement. Any other detection method could be considered. For a detection method of the PHmetry type, pH detection electrodes could be integrated into the device.

Some of the above steps are however optional, the analysis method can therefore take different possible configurations.

• E1 : Concentration,
• E2 : Lavage,
• E3 : Apport d'un milieu de culture,
• E4 : Culture
• E5 : Suivi optique de croissance lors de la culture et comptage des colonies,

In a first C1 configuration ( figure 1 ), the process may include the following steps:

• E1: Concentration,
• E2: Washing,
• E3: Contribution of a culture medium,
• E4: Culture
• E5: Optical growth monitoring during culture and counting of colonies,

In a configuration C1 ′ taking up steps E1 to E5 of the first configuration, a step E5 ′ can be added after step E5 in order to collect bacteria for treatment.

• E1 : Concentration,
• E2 : Lavage,
• E3 : Apport d'un milieu de culture,
• E4 : Culture,
• E6 : Lavage,
• E7 : Lyse,
• E8 : Séparation,
• E9 : Détection par amplification.

In a second C2 configuration ( figure 1 ), the process may include the following steps:

• E1: Concentration,
• E2: Washing,
• E3: Contribution of a culture medium,
• E4: Culture,
• E6: Washing,
• E7: Lyse,
• E8: Separation,
• E9: Detection by amplification.

Likewise, in a configuration C2 ′ taking up steps E1 to E8 of configuration C2, a step E8 ′, replacing step E9, can be added. This step consists in taking out the separated DNA for detection / storage, in particular with a view to DNA sequencing.

• E1 : Concentration,
• E3 : Apport d'un milieu de culture,
• E4+E5 : Culture/Suivi de croissance,
• E6 : Lavage,
• E7 : Lyse,
• E8 : Séparation,
• E9 : Détection par amplification.

In a third configuration C3 ( figure 1 ), the process may include the following steps:

• E1: Concentration,
• E3: Contribution of a culture medium,
• E4 + E5: Culture / Growth monitoring,
• E6: Washing,
• E7: Lyse,
• E8: Separation,
• E9: Detection by amplification.

• E1 : Concentration,
• E6 : Lavage, élimination des inhibiteurs de PCR,
• E7 : Lyse,
• E8 : Séparation,
• E9 : Détection par amplification.

In a last configuration C4, it is also possible to dispense with steps E2 to E5. We thus have:

• E1: Concentration,
• E6: Washing, elimination of PCR inhibitors,
• E7: Lyse,
• E8: Separation,
• E9: Detection by amplification.

In this C4 configuration, the variant including step E8 ′ is also possible, with a view to bringing out the released DNA.

The invention aims to provide a microfluidic device whose architecture is suitable for implementing at least two of the configurations described above.

With reference to figures 2A to 2C , the microfluidic device comprises a single rigid support S. The figure 6 described below gives an exemplary embodiment of the device.

This rigid support S integrates a microfluidic network suitable for implementing the steps of the analysis process. It will be seen that the microfluidic network can take different architectures depending on the configuration of the analysis method which is implemented.

The support S advantageously comprises a flat lower wall and an architecture with several superimposed layers along said main axis, stacked on its lower wall.

The microfluidic network of the device comprises two units U1, U2 or three units U1, U2, U3 each used for the implementation of one or more of the steps of the analysis method, depending on the configuration of the method which is chosen.

In the device of the invention, the culture of the biological species is carried out in a thin layer, that is to say with a volume which may range from 1 μL to 1 mL. The advantage of carrying out a culture in a thin layer is that the colonies can be visible much more quickly (duration of the order of 2 to 3 hours) than with a culture carried out in a conventional mode. By combining a step of concentration of the cells and a culture in a thin layer, it is thus possible to analyze samples very weakly loaded with cells. It is thus possible, for example, to analyze large volumes of water, with a view to controlling the level of contamination.

Moreover, thanks to the device, it is possible to carry out the entire stage of purification of the DNA molecules then their transfer to another chamber for amplification in its entirety, without a dilution stage and without any risk of contamination.

In the three alternative embodiments proposed and shown on the figures 2A to 2C , The first unit U1 comprises a first chamber 10 formed in said support. This chamber 10 has a non-zero volume and is delimited by the walls of the support S.

The first unit U1 comprises a first channel 11 formed in the support for injecting fluids into the first chamber 10 or for discharging fluids outside this first chamber. The first channel 11 has a first end comprising an opening formed for example through an upper wall of the support S and a second end which opens into said first chamber 10. The first end of the first channel is for example arranged vertically and its second end opens out. for example horizontally in the first chamber 10.

The first unit U1 comprises a second channel 12. This second channel 12 also comprises a first end which communicates with the outside, forming an opening made for example through an upper wall of the support S and a second end which communicates with the space. formed by the first chamber 10. Via this second channel 12, it is also possible to inject fluids into said first chamber or to evacuate fluids outside of said first chamber. Its first end is for example arranged vertically and its second end horizontally. The first chamber 10 is placed between the first channel 11 and the second channel 12.

Upwards, the first chamber 10 can be closed by a flexible and stretchable membrane 13. At the level of the first chamber, an upper wall of the support thus comprises an opening which is hermetically covered by said membrane 13. The membrane 13 is thus anchored in the support by any suitable fixing solution, for example by gluing. This membrane 13 will for example be composed of a film, for example of the MicroAmp, 3M (registered trademarks) type, of thickness, dimensions and constitution adapted to deform in a hyper-elastic manner, with respect to its points of anchoring, at least to the bottom of the first chamber.

The membrane 13 is capable of reversibly deforming between several configurations. It can stretch by hyper-elastic deformation towards the outside of the support S, retract inside the first chamber 10 by compression, or be at rest. By hyper-elastic material is meant a material capable of presenting a surface capable of passing from a first surface to a second surface, the second surface being equal to at least 5 times the first surface area, for example 10 times or even to 50 times the first area.

The first unit U1 also comprises a transverse filter 14 arranged in said first chamber 10 and separating said first chamber 10 into two spaces. 100, 101. The two spaces are for example superimposed and thus designated the lower space 100 located under the filter 14 and the upper space 101 located above the filter 14. This filter 14 is preferably produced in whole or in part in the form of a flexible and thin film, drawn in the space formed by the chamber so as to allow passage from one space to another only through the pores of the filter 14. The film has elastic deformability allowing it to stretch during the exercise of a support force in a substantially vertical direction, this elastic deformability having a level sufficient to reach the bottom of the chamber 10. The filter 14 has an average pore diameter of between 0.2 μm and 50 μm, for example between 0.2 µm and 1 µm for the separation of microorganisms. The diameter of the pores is of course adapted to ensure separation between different biological species present in the sample. The filter 14 will for example be composed of a film of thickness, dimensions and constitution adapted to deform to the bottom of the chamber 10 relative to its anchoring points. It may have the same hyper-elasticity characteristics as the membrane.

According to one feature, the first channel 11 opens into the upper space 101 of the first chamber 10 and the second channel 12 opens into the lower space 100 of the first chamber 10. The mouths of the two channels are therefore separated by the filter 14. arranged in the bedroom.

With reference to figures 2B and 2C , the first unit U1 can advantageously comprise a rough bearing surface 15 arranged on the bottom of the first chamber 10. This rough bearing surface 15 extends over a majority part of the bottom of the first chamber. It includes an average surface roughness parameter between 0.1 μm and 10 μm, preferably between 0.2 μm and 3 μm. This rough bearing surface 15 is intended to allow mechanical lysis of the biological species present in a biological sample placed in the device. Preferably, the mechanical lysis is carried out by grinding said biological species, by abrasion on said rough bearing surface. The grinding operation is carried out by a friction movement of the biological species against the rough bearing surface, using a suitable grinding member. This member will for example be a spatula or a rod, for example made of plastic or metallic material. This member is applied from the outside of the chamber 10 and its end is applied against the outer surface of the membrane 13 so as to stretch the membrane 13 and the filter 14 towards the bottom of the first chamber 10 and thus rub the biological species. present in a sample against the rough bearing surface 15.

The second unit U2 of the device for its part comprises a second chamber 20 of non-zero volume, delimited by the walls of the support S. The second unit U2 also comprises a third channel 21 formed in said support. This third channel 21 has a first end comprising an opening formed for example through an upper wall of the support and a second end which opens only into said second chamber 20. The first end of this third channel 21 is for example arranged vertically and its second end opens for example horizontally into the second chamber 20. The first end of this third channel is for example closed by a hydrophobic membrane 210, that is to say impermeable to liquid but permeable to gas such as air. This hydrophobic membrane 210 can be made from a material of the PTFE (Polytetrafluoroethylene) type.

Two transverse walls of the support, advantageously a parallel upper wall 200 and a lower wall 201, partially delimiting the second chamber 20, are made of a transparent material, thus making it possible to carry out an optical reading through the volume of the second chamber. The term “transparent” is understood to mean that the material used is at least partially transparent to visible light, so as to allow at least 80% of this light to pass. It should therefore be understood that it will be transparent enough to see the interior of the chamber. The lower wall may be made of glass and the upper wall may be formed of a removable adhesive bonded to close said second chamber from the upper side.

According to a particular feature of the invention, the device also comprises a first transfer channel 22 formed in said support. This first transfer channel 22 is intended to connect the first chamber 10, more precisely its lower space 100, to the second chamber 20.

The first transfer channel 22 has a first end opening directly into the second channel 12, thus forming a bypass node on this second channel 12. It has a second end opening directly into the second chamber.

• vers l'extérieur uniquement via le deuxième canal uniquement ou,
• vers la deuxième chambre uniquement à travers le premier canal de transfert.

The device further comprises switching means which can for example be arranged on the second channel 12 to select the connection of the first chamber:

• to the outside only via the second channel only or,
• to the second chamber only through the first transfer channel.

These switching means may consist of a hollow removable cone 120 in the form of a funnel. When it is inserted by its tip into the second channel 12, it allows communication between the outside and the first chamber and its wall closes the entrance to the first transfer channel 22, made at the bypass node. When removed, the first end of the second channel 12 may be sealed, for example by means of an adhesive 121 applied to a surface of the support and the connection between the first transfer channel 22 and the second channel 12 is then open, allowing a fluid to circulate between the first chamber 10 and the second chamber 20.

• Dans une première position, permet d'autoriser l'accès au-deuxième canal en obturant l'embouchure du canal de transfert 22 au niveau du nœud de dérivation,
• Dans une deuxième position, permet d'ouvrir la liaison entre le deuxième canal 12 et le canal de transfert 22.

Of course, the switching means can be produced according to other variant embodiments. The general principle being to be able to access the first chamber by closing off the transfer channel or to allow a connection between the first chamber and the second chamber. It can thus be a simple valve which:

• In a first position, allows access to the second channel by blocking the mouth of the transfer channel 22 at the bypass node,
• In a second position, opens the connection between the second channel 12 and the transfer channel 22.

In an architecture with only two units U1, U2 as described above, the method can be implemented according to the first configuration or the second configuration described above.

• E1 : L'échantillon liquide ECH est injecté par le deuxième canal 12, par exemple à l'aide d'une pipette vers la première chambre 10 à travers le cône 120. Le cône 120 est agencé dans le deuxième canal à une profondeur suffisante pour obturer l'entrée du premier canal de transfert 22, au niveau du nœud de dérivation. Dans le même temps, le premier canal 11 est ouvert sur l'extérieur pour remplir le rôle d'évent lors du remplissage de la première chambre 10 et pour évacuer le liquide filtré. Lors de l'injection, sous l'effet de la pression d'injection, l'échantillon est filtré par le filtre 14. Les espèces biologiques 4 d'intérêt sont maintenues dans l'espace inférieur 100 de la première chambre 10 et le reste est évacué vers l'extérieur du dispositif par le premier canal 11.
• E2 : Dans la même configuration, l'étape de lavage (optionnelle) est ensuite mise en œuvre. Un liquide de lavage L est injecté par le deuxième canal 12, à travers le cône, pour purifier les espèces biologiques 4 capturées dans l'espace inférieur 100 de la première chambre 10. Ce liquide de lavage est évacué à travers le premier canal 11.
• E3 : Un milieu de culture MC est injecté par le premier canal 11 pour pénétrer dans la première chambre 10. L'entrée/sortie du deuxième canal 12 est fermée par l'adhésif 121 et le premier canal de transfert 22 est ouvert, permettant une communication étanche, sans risque de contamination, entre la première chambre 10 et la deuxième chambre 20.
• E3 : Les espèces biologiques 4 dans leur milieu de culture MC sont transférés vers la deuxième chambre 20 via le premier canal de transfert 22. Pour le transfert, une pression d'air P peut être appliquée dans le premier canal 11. Le troisième canal 21 est obturé grâce à la membrane 210 hydrophobe, permettant à l'air de s'évacuer lors du transfert et d'éviter au liquide de s'échapper. L'étape de culture peut durer 16 heures, en chauffant la deuxième chambre 20 à une température de 37°C.
• E4 - E5 : Un dispositif de lecture optique LO est activé pour réaliser un suivi de la culture des espèces biologiques présentes dans la deuxième chambre 20. La lecture optique est permise grâce à la transparence des deux parois 200, 201 parallèles délimitant la deuxième chambre 20.

In the first configuration C1 of the method implemented in the device of the figure 2A and with reference to figures 3A to 3D , the steps are then as follows:

• E1: The liquid sample ECH is injected through the second channel 12, for example using a pipette to the first chamber 10 through the cone 120. The cone 120 is arranged in the second channel at a depth sufficient to block the entry of the first transfer channel 22, at the branch node. At the same time, the first channel 11 is open to the outside to fulfill the role of a vent when filling the first chamber 10 and to evacuate the filtered liquid. During injection, under the effect of the injection pressure, the sample is filtered by the filter 14. The biological species 4 of interest are maintained in the lower space 100 of the first chamber 10 and the remainder is evacuated to the outside of the device via the first channel 11.
• E2: In the same configuration, the washing step (optional) is then implemented. A washing liquid L is injected through the second channel 12, through the cone, to purify the biological species 4 captured in the lower space 100 of the first chamber 10. This washing liquid is evacuated through the first channel 11.
• E3: An MC culture medium is injected through the first channel 11 to enter the first chamber 10. The inlet / outlet of the second channel 12 is closed by the adhesive 121 and the first transfer channel 22 is opened, allowing a sealed communication, without risk of contamination, between the first chamber 10 and the second chamber 20.
• E3: The biological species 4 in their culture medium MC are transferred to the second chamber 20 via the first transfer channel 22. For the transfer, an air pressure P can be applied in the first channel 11. The third channel 21 is sealed by the hydrophobic membrane 210, allowing air to escape during transfer and prevent liquid from escaping. The cultivation step can last 16 hours, heating the second chamber 20 to a temperature of 37 ° C.
• E4 - E5: An optical reading device LO is activated to monitor the culture of the biological species present in the second chamber 20. Optical reading is enabled thanks to the transparency of the two parallel walls 200, 201 delimiting the second chamber 20 .

• E1 : L'échantillon liquide ECH est injecté par le deuxième canal 12, par exemple à l'aide d'une pipette vers la première chambre 10 à travers le cône 120. Le cône est agencé dans le deuxième canal 12 à une profondeur suffisante pour obturer l'entrée du premier canal de transfert 21, au niveau du nœud de dérivation. Dans le même temps, le premier canal 11 est ouvert sur l'extérieur pour remplir le rôle d'évent lors du remplissage de la première chambre 10 et pour évacuer le liquide filtré. Lors de l'injection, sous l'effet de la pression d'injection, l'échantillon ECH est filtré par le filtre 14. Les espèces biologiques 4 d'intérêt sont maintenues dans l'espace inférieur 100 de la première chambre 10 et le reste est évacué vers l'extérieur par le premier canal 11.
• E2 : L'étape de lavage (optionnelle) est ensuite mise en œuvre. Un liquide de lavage L est injecté par le deuxième canal 12, à travers le cône 120, pour purifier les espèces biologiques 4 capturées dans l'espace inférieur 100 de la première chambre 10. Ce liquide de lavage L est évacué vers l'extérieur à travers le premier canal 11.
• E3 : Un milieu de culture MC est injecté par le premier canal 11 pour pénétrer dans la première chambre 10.
• E4 : La culture est réalisée dans la première chambre 10. L'étape de culture peut durer 4 heures, en chauffant la première chambre 10 à une température de 37°C.
• E6 : Un liquide de lavage L est injecté par le deuxième canal pour laver les espèces biologiques présentes dans l'espace inférieur de la première chambre.
• E7 Une lyse des espèces biologiques 4 est réalisée dans la première chambre. Cette lyse consiste à broyer les espèces biologiques 4 contre la surface d'appui rugueuse 15 présente au fond de la première chambre 10.
• E8 : Le canal de transfert 22 entre les deux chambres est ouvert. Un réactif d'amplification RA est injecté par le premier canal 11 pour réaliser une élution du matériel biologique 40 obtenu après lyse et transférer le liquide d'intérêt vers la deuxième chambre 20, via le canal de transfert 22.
• Une pression P peut être appliquée à travers le premier canal 11 pour réaliser le transfert du liquide d'intérêt vers la deuxième chambre 20.
• Une réaction d'amplification est mise en œuvre dans la deuxième chambre pendant 45 minutes, en chauffant la deuxième chambre à une température de 60°C. Un dispositif de lecture optique LO est activé pour réaliser une détection de pathogènes dans la deuxième chambre 20. La lecture optique est permise grâce à la transparence des deux parois 200, 201 parallèles délimitant la deuxième chambre.

In the second configuration C2 of the method, implemented in the device of the figure 2B , and with reference to figures 4A to 4H , the steps are then as follows:

• E1: The liquid sample ECH is injected through the second channel 12, for example using a pipette to the first chamber 10 through the cone 120. The cone is arranged in the second channel 12 at a depth sufficient to block the entry of the first transfer channel 21, at the bypass node. At the same time, the first channel 11 is open to the outside to fulfill the role of a vent when filling the first chamber 10 and to evacuate the filtered liquid. During the injection, under the effect of the injection pressure, the ECH sample is filtered by the filter 14. The biological species 4 of interest are maintained in the lower space 100 of the first chamber 10 and the remainder is discharged to the outside by the first channel 11.
• E2: The washing step (optional) is then implemented. A washing liquid L is injected through the second channel 12, through the cone 120, to purify the biological species 4 captured in the lower space 100 of the first chamber 10. This washing liquid L is discharged to the outside at through the first channel 11.
• E3: An MC culture medium is injected through the first channel 11 to enter the first chamber 10.
• E4: The culture is carried out in the first chamber 10. The culture step can last 4 hours, by heating the first chamber 10 to a temperature of 37 ° C.
• E6: A washing liquid L is injected through the second channel to wash the biological species present in the lower space of the first chamber.
• E7 Lysis of biological species 4 is carried out in the first chamber. This lysis consists in grinding the biological species 4 against the rough bearing surface 15 present at the bottom of the first chamber 10.
• E8: The transfer channel 22 between the two chambers is open. An amplification reagent RA is injected through the first channel 11 to elute the biological material 40 obtained after lysis and transfer the liquid of interest to the second chamber 20, via the transfer channel 22.
• A pressure P can be applied through the first channel 11 to effect the transfer of the liquid of interest to the second chamber 20.
• An amplification reaction is carried out in the second chamber for 45 minutes, heating the second chamber to a temperature of 60 ° C. An optical reading device LO is activated to detect pathogens in the second chamber 20. Optical reading is enabled thanks to the transparency of the two parallel walls 200, 201 delimiting the second chamber.

With reference to the figure 2C , the device can advantageously comprise a third unit U3, allowing it to implement the method according to the third configuration C3 described above. The third unit U3 comprises a third chamber 30 of non-zero volume, integrated into said support S. The third unit U3 comprises a fourth channel 31 formed in the support S to inject fluids into the third chamber 30 or to evacuate fluids outside of it. this third chamber 30. The fourth channel 31 comprises a first end having an opening formed for example through an upper wall 12 of the support and a second end which opens into said third chamber 30. The first end of the first channel 31 is for example arranged vertically and its second end opens for example horizontally into the third chamber 30. The first end of this fourth channel 31 is for example closed by a hydrophobic membrane 310, that is to say impermeable to liquid but permeable to gas such as 'air. This hydrophobic membrane can be made from a material of the PTFE (Polytetrafluoroethylene) type.

Two walls of the support, advantageously an upper wall 300 and a lower wall 301, delimiting the third chamber 30, are made of a transparent material, thus making it possible to carry out an optical reading through this third chamber. The term “transparent” is understood to mean that the material used is at least partially transparent to visible light, so as to allow at least 80% of this light to pass. It should therefore be understood that it will be transparent enough to see the interior of the chamber. The lower wall may be made of glass and the upper wall may be formed of a removable adhesive bonded to close said third chamber from the upper side.

According to a feature of the invention, in this variant of the figure 2C , the device also comprises a second transfer channel 32 formed in said support S. This second transfer channel 32 is intended to connect the first chamber 10, more precisely its upper space 101, to the third chamber 30.

Advantageously, the second transfer channel 32 has a first end opening directly into the first channel 11, thus forming a bypass node on this first channel 11 (symmetrically to the first transfer channel). It has a second end opening directly into the third chamber 30.

• vers l'extérieur uniquement via le premier canal ou,
• vers la troisième chambre uniquement à travers le deuxième canal de transfert.

As for the first transfer channel, the device further comprises routing means that can for example be arranged on the first channel 11 to select the connection of the first chamber:

• to the outside only via the first channel or,
• to the third chamber only through the second transfer channel.

These switching means may also consist of a hollow removable cone 110 in the form of a funnel. When it is inserted into the first channel 11, it allows communication between the outside and the first chamber 10 and its wall closes the entrance to the second transfer channel 32, made at the bypass node. When it is removed, the first end of the first channel 12 is sealed, for example using an adhesive 111 applied to a surface of the support and the connection between the second transfer channel 32 and the first channel 11 is then open, allowing fluid to flow between the first chamber 10 and the third chamber 30.

As for the first switching means, it is understood that other means can be used, the objective being to have a solution to access the first chamber, by blocking the second transfer channel or to authorize the connection. from the first chamber to the third chamber, through the second transfer channel. The two-position valve-type switching means, described above, can be used in an identical manner.

• E1 : L'échantillon liquide ECH est injecté par le deuxième canal 12, par exemple à l'aide d'une pipette à travers le cône 120 vers la première chambre 10. Le cône 120 est agencé dans le deuxième canal 12 à une profondeur suffisante pour obturer l'entrée du premier canal de transfert 22, au niveau du nœud de dérivation. Dans le même temps, le premier canal 11 est ouvert sur l'extérieur pour remplir le rôle d'évent lors du remplissage de la première chambre 10 et pour évacuer le liquide filtré. Lors de l'injection, sous l'effet de la pression d'injection, l'échantillon ECH est filtré par le filtre 14. Les espèces biologiques 4 d'intérêt sont maintenues dans l'espace inférieur 100 de la première chambre 10 et le reste est évacué vers l'extérieur par le premier canal 11.
• L'étape de lavage (optionnelle-non représentée) est ensuite mise en œuvre.

In the third configuration C3 of the method implemented in the device of the figure 2C and with reference to figures 5A to 5F , the steps are then as follows:

• E1: The liquid sample ECH is injected through the second channel 12, for example using a pipette through the cone 120 towards the first chamber 10. The cone 120 is arranged in the second channel 12 at a sufficient depth to block the entry of the first transfer channel 22, at the branch node. At the same time, the first channel 11 is open to the outside to fulfill the role of a vent when filling the first chamber 10 and to evacuate the filtered liquid. During injection, under the effect of the injection pressure, the ECH sample is filtered by the filter 14. The biological species 4 of interest are maintained in the lower space 100 of the first chamber 10 and the remainder is discharged to the outside through the first channel 11.
• The washing step (optional - not shown) is then implemented.

• E3 : Un milieu de culture MC est injecté par le premier canal 11 pour pénétrer dans la première chambre 10. L'entrée/sortie du deuxième canal 12 est fermée par l'adhésif 121 et le premier canal de transfert 22 est ouvert, permettant une communication étanche, sans risque de contamination, entre la première chambre 10 et la deuxième chambre 20.
• E3 : Les espèces biologiques 4 dans leur milieu de culture MC sont transférées vers la deuxième chambre 20 via le premier canal de transfert 22. Pour le transfert, une pression d'air P peut être appliquée dans le premier canal. Le troisième canal 21 est obturé grâce à la membrane 210 hydrophobe, permettant à l'air de s'évacuer lors du transfert et d'éviter au liquide de s'échapper.
• E4 - E5 : L'étape de culture peut durer 4 heures, en chauffant la première chambre à une température de 37°C. Un suivi optique de la culture est mis en œuvre à travers la deuxième chambre 20, à l'aide d'un dispositif de lecture optique LO. Cette première étape de lecture permet de s'assurer que la culture est efficace. A titre d'exemple, si dans le cas d'un test de stérilité, aucune bactérie n'est détectée en culture dans la deuxième chambre 20, il est inutile de poursuivre le procédé et de réaliser la purification et l'amplification de l'ADN bactérien. Cette démarche permet alors de minimiser le coût global de l'analyse.
• E6 : Si l'analyse est poursuivie, un liquide de lavage L est injecté par le troisième canal 21 pour laver les espèces biologiques 4 présentes dans la deuxième chambre 20 et pour transférer l'échantillon vers la première chambre 10, à travers le premier canal de transfert 22. Le cône 110 est en place pour fermer l'accès à la troisième chambre 30 via le deuxième canal de transfert 32.
• E7 : Une lyse des espèces biologiques 4 est réalisée dans la première chambre 10. Cette lyse consiste à broyer les espèces biologiques 4 contre la surface d'appui rugueuse 15 présente au fond de la première chambre 10.
• E8 : Le deuxième canal de transfert 32 est ouvert. Un réactif d'amplification RA est injecté par le deuxième canal 12 pour réaliser une élution du matériel biologique obtenu après lyse et transférer le liquide d'intérêt de la première chambre 10 vers la troisième chambre 30.
• Une pression P peut être appliquée à travers le deuxième canal pour réaliser le transfert du liquide d'intérêt vers la troisième chambre.
• Une réaction d'amplification est mise en œuvre dans la troisième chambre pendant 45 minutes, en chauffant la deuxième chambre à une température de 60°C. Un dispositif de lecture optique est activé pour réaliser une détection de pathogènes dans la troisième chambre. La lecture optique est permise grâce à la transparence des deux parois parallèles délimitant la troisième chambre.

A washing liquid is injected through the second channel, through the cone, to purify the biological species captured in the lower space of the first chamber. This washing liquid is discharged through the first channel.

• E3: An MC culture medium is injected through the first channel 11 to enter the first chamber 10. The inlet / outlet of the second channel 12 is closed by the adhesive 121 and the first transfer channel 22 is opened, allowing a sealed communication, without risk of contamination, between the first chamber 10 and the second chamber 20.
• E3: The biological species 4 in their MC culture medium are transferred to the second chamber 20 via the first transfer channel 22. For the transfer, an air pressure P can be applied in the first channel. The third channel 21 is closed thanks to the hydrophobic membrane 210, allowing the air to escape during the transfer and to prevent the liquid from escaping.
• E4 - E5: The culture step can last 4 hours, heating the first chamber to a temperature of 37 ° C. Optical monitoring of the culture is implemented through the second chamber 20, using an optical reading device LO. This first reading step ensures that the culture is effective. By way of example, if in the case of a sterility test, no bacteria are detected in culture in the second chamber 20, it is unnecessary to continue the process and to carry out the purification and the amplification of the. Bacterial DNA. This approach then makes it possible to minimize the overall cost of the analysis.
• E6: If the analysis is continued, a washing liquid L is injected through the third channel 21 to wash the biological species 4 present in the second chamber 20 and to transfer the sample to the first chamber 10, through the first channel transfer 22. The cone 110 is in place to close access to the third chamber 30 via the second transfer channel 32.
• E7: A lysis of the biological species 4 is carried out in the first chamber 10. This lysis consists in grinding the biological species 4 against the rough bearing surface 15 present at the bottom of the first chamber 10.
• E8: The second transfer channel 32 is open. An RA amplification reagent is injected through the second channel 12 to elute the biological material obtained after lysis and transfer the liquid of interest from the first chamber 10 to the third chamber 30.
• A pressure P can be applied through the second channel to effect the transfer of the liquid of interest to the third chamber.
• An amplification reaction is carried out in the third chamber for 45 minutes, heating the second chamber to a temperature of 60 ° C. An optical reading device is activated to perform pathogen detection in the third chamber. Optical reading is enabled thanks to the transparency of the two parallel walls delimiting the third chamber.

The versatility of the device of the invention is better understood, whether in its architecture with two units U1, U2 or with three units U1, U2, U3.

• Dans la première configuration C1 du procédé ou dans la configuration C1', la première unité U1 peut être employée pour les étapes E1, E2 et E3 et la deuxième unité U2 pour les étapes E4 et E5.
• Dans la deuxième configuration C2 du procédé ou dans la configuration C2', la première unité U1 peut être employée pour les étapes E1, E2, E3, E4, E6, E7 et E8 et la deuxième unité U2 pour l'étape E9.
• Dans la troisième configuration C3 du procédé, la première unité U1 peut être employée pour les étapes E1, E3, E6, E7 et E8, la deuxième unité U2 pour les étapes E4 et E5 et la troisième unité pour l'étape E9.
• Dans la configuration C4 du procédé, la première unité U1 peut être employée pour les étapes E1, E6, E7, E8 et la deuxième unité pour l'étape E9.

In summary :

• In the first configuration C1 of the process or in the configuration C1 ', the first unit U1 can be used for the steps E1, E2 and E3 and the second unit U2 for the steps E4 and E5.
• In the second configuration C2 of the method or in the configuration C2 ', the first unit U1 can be used for steps E1, E2, E3, E4, E6, E7 and E8 and the second unit U2 for step E9.
• In the third configuration C3 of the method, the first unit U1 can be used for steps E1, E3, E6, E7 and E8, the second unit U2 for steps E4 and E5 and the third unit for step E9.
• In the process configuration C4, the first unit U1 can be used for steps E1, E6, E7, E8 and the second unit for step E9.

The two transfer channels allow easy switching from one unit to another, while avoiding contamination.

The device can advantageously integrate means for heating the internal space of each chamber, composed for example of at least one heating resistor 19 or of a Peltier element, as shown in the appended figures. The resistance is for example fixed under the lower wall of the housing. A power source 20 will for example be provided to power the resistor 19. The power source will for example include one or more electric cells, providing sufficient energy to heat the chamber to a temperature within the range defined above. , i.e. 20 ° C to 100 ° C. Of course, other heating means could be used, comprising for example a conductive ink deposited by printing or screen printing under the lower wall of the housing. These heating means are used to heat the chamber to a given temperature during a stage of culture of biological species or during an amplification reaction.

In a nonlimiting manner, in its variant of the figure 2B , the device can be produced according to the architecture shown in figure 6 .

• Le support comporte une lame 50, par exemple en verre ou en en matériau plastique, de type PMMA ou COC ;
• La lame 50 est recouverte dans une première zone d'une surface abrasive de manière à former sur une partie de sa face supérieure la surface d'appui rugueuse 15 dédiée à la lyse ;
• Dans au moins une deuxième zone la lame 50 est transparente pour former la paroi inférieure 201 transparente de la deuxième chambre 20, destinée à la lecture optique ;
• Une première couche 51 portant une première empreinte micro-fluidique est déposée sur la face supérieure de la lame 50, cette première empreinte comportant une première cavité définissant l'espace inférieur 100 de la première chambre 10, une deuxième cavité définissant une partie inférieure de la deuxième chambre 20 et la partie inférieure du troisième canal 21 ; la première cavité a ses bords agencés autour de la première zone abrasive et la deuxième cavité a ses bords agencés autour de la deuxième zone de lecture ;
• Le filtre 14 est apposé sur la première couche pour recouvrir l'espace inférieur 100 de la première chambre et la membrane hydrophobe 210 est apposée sur la partie inférieure du troisième canal 21 ;
• Une deuxième couche 52 portant une deuxième empreinte micro-fluidique est déposée sur la face supérieure de la première couche 51, en recouvrant également le filtre 14 et la membrane hydrophobe 210. Cette deuxième empreinte micro-fluidique comporte une cavité formant l'espace supérieur 101 de la première chambre 10, une deuxième cavité formant une partie médiane de la deuxième chambre 20 et la partie supérieure du troisième canal 21 ;
• Une troisième couche 53 portant une troisième empreinte micro-fluidique est déposée sur la face supérieure de la deuxième couche 52 ; Cette troisième empreinte micro-fluidique comporte la partie supérieure de la première chambre 10 et la partie supérieure de la deuxième chambre 20 ;
• Une lame de verre ou en matériau plastique est dimensionnée pour recouvrir la face supérieure de la troisième couche 53 au niveau de la deuxième chambre, formant la paroi supérieure 200 transparente du support ;
• Un capot 54, par exemple en PMMA, est positionné au-dessus de la première chambre 10 ; Sur sa face inférieure, le capot comporte la membrane 13 destinée à refermer la première chambre par le dessus ;
• Le capot comporte une ouverture axiale supérieure, permettant d'accéder à la membrane 13, pour effectuer la lyse ;
• Le capot 54 comporte deux entrées/sorties fluidiques sur sa face supérieure. La première entrée/sortie est reliée à un premier canal axial traversant formé à travers la membrane 13 et les trois couches et débouchant dans la première chambre 10 pour former le premier canal 11 du support ; La deuxième entrée/sortie est reliée à un deuxième canal axial traversant formé à travers la membrane 13 et la deuxième et troisième couches et débouchant au-dessus de la membrane hydrophobe 210, pour former le troisième canal 21 du support ;
• Le support comporte enfin deux autres canaux traversants formant le premier canal de transfert 22 reliant les deux chambres 10, 20 ;
• Deux autres couches 55, 56 permettent de réaliser l'entrée du deuxième canal 12 et la jonction du canal de transfert 22 sur ce deuxième canal 12 ;

On this figure 6 , the S support has the following features:

• The support comprises a blade 50, for example made of glass or of plastic material, of the PMMA or COC type;
• The blade 50 is covered in a first zone with an abrasive surface so as to form on a part of its upper face the rough bearing surface 15 dedicated to the lysis;
• In at least a second zone the blade 50 is transparent to form the transparent lower wall 201 of the second chamber 20, intended for optical reading;
• A first layer 51 bearing a first microfluidic imprint is deposited on the upper face of the blade 50, this first imprint comprising a first cavity defining the lower space 100 of the first chamber 10, a second cavity defining a lower part of the second chamber 20 and the lower part of the third channel 21; the first cavity has its edges arranged around the first abrasive zone and the second cavity has its edges arranged around the second reading zone;
• The filter 14 is affixed to the first layer to cover the lower space 100 of the first chamber and the hydrophobic membrane 210 is affixed to the lower part of the third channel 21;
• A second layer 52 bearing a second microfluidic imprint is deposited on the upper face of the first layer 51, also covering the filter 14 and the hydrophobic membrane 210. This second microfluidic imprint comprises a cavity forming the upper space 101. of the first chamber 10, a second cavity forming a middle part of the second chamber 20 and the upper part of the third channel 21;
• A third layer 53 bearing a third microfluidic imprint is deposited on the upper face of the second layer 52; This third microfluidic footprint comprises the upper part of the first chamber 10 and the upper part of the second chamber 20;
• A glass or plastic slide is sized to cover the upper face of the third layer 53 at the level of the second chamber, forming the transparent upper wall 200 of the support;
• A cover 54, for example made of PMMA, is positioned above the first chamber 10; On its lower face, the cover comprises the membrane 13 intended to close the first chamber from above;
• The cover has an upper axial opening, allowing access to the membrane 13, to perform the lysis;
• The cover 54 has two fluidic inlets / outlets on its upper face. The first inlet / outlet is connected to a first through axial channel formed through the membrane 13 and the three layers and opening into the first chamber 10 to form the first channel 11 of the support; The second inlet / outlet is connected to a second through axial channel formed through the membrane 13 and the second and third layers and opening above the hydrophobic membrane 210, to form the third channel 21 of the support;
• The support finally comprises two other through channels forming the first transfer channel 22 connecting the two chambers 10, 20;
• Two other layers 55, 56 make it possible to make the entry of the second channel 12 and the junction of the transfer channel 22 on this second channel 12;

In the three-chamber variant of the figure 2C , the architecture of the support would be similar, the production principles of the third chamber 30 and of the second transfer channel 32 being modeled on those of the second chamber 20 and of the first transfer channel 22.

Advantageously, the second chamber 20 in the variant with only two units ( figures 2A and 2B ) and the second chamber 20 and / or the third chamber 30 in the three-unit variant ( figure 2C ), has a suitably shaped internal volume, either to ensure reliable control of the amplification reaction or to identify multiple targets simultaneously. In the latter case, the chamber can be shaped to allow identification of several targets simultaneously. These so-called multiplex tests are for example used to detect groups of pathogenic organisms corresponding to similar clinical symptoms or to detect a bacterium but also its potential genes for resistance to antibiotics.

In the remainder of the description, we will describe the architecture of a so-called amplification chamber 25 in general. This architecture can be applied to the second chamber 20 and / or to the third chamber 30 of the device of the invention already described above.

• Optimiser la fluidique (absence de bulles) ;
• Pousser l'air hors du composant mais retenir le liquide ;
• Ne pas contaminer l'environnement ;
• Permettre le multiplexage ;
• Accueillir un contrôle interne de réaction ;
• Limiter les volumes morts ;
• Ne pas diviser l'échantillon ;

This amplification chamber has been designed to meet several objectives:

• Optimize fluidics (absence of bubbles);
• Push the air out of the component but retain the liquid;
• Do not contaminate the environment;
• Allow multiplexing;
• Host an internal reaction control;
• Limit dead volumes;
• Do not divide the sample;

The principle is to create at least one Ax alcove (x ranging from 1 to N, N corresponding to the number of alcoves and being greater than or equal to 1) in the amplification chamber, to house there an internal control compound of the reaction (for example a selected DNA sequence or amplification primers targeting a predefined DNA) adapted to the amplification technology used (PCR, LAMP RPA, etc.). According to this principle, either the DNA is dried in the alcove, the primers are then brought by the liquid introduced by the chamber, or the primers are dried in the alcove and the DNA is brought by the liquid introduced into the chamber. .

In the case of an internal reaction control, the internal control compound can be placed in the Ax alcove at a known concentration and then dried directly in the chamber. It thus remains permanently in the device and is ready for use.

The advantage of depositing the control compound not directly in the optical reading zone but outside it makes it possible, in addition to optimizing the gas exchange space, to differentiate the control amplification from the target amplification. The control amplification will in fact be both temporally and spatially shifted.

The architecture of the device in several layers makes it possible to produce the amplification chamber with layers of different designs. The lower layer can in fact include one or more alcoves and the upper layers of the chamber define the total optical reading cross section of the chamber. This principle in several layers is illustrated by the figure 7 . On this figure 7 , we can see a lower layer S1 carrying the alcove A1 and an upper layer S2 defining the optical reading cross section (shown here without limitation with a rectangular shape). The alcove A1 is here in the shape of a half moon. It is understood from this principle that the liquid penetrates throughout the chamber and that it can spread throughout the volume defined by the several layers, making it possible not to disturb the optical reading and to obtain the spatial and temporal shift described above. above.

The figures 8A to 8C show different architectures of the amplification chamber stratum. In these figures, the optical reading zone Z is shown in gray. On the figure 8A , the lower layer S1 has a protrusion forming the alcove A1 going beyond the section of the optical reading zone Z of the chamber in the transverse plane, opposite the point of entry of liquid into the chamber ( corresponding to the design of the figure 7 ). This remote zone makes it possible to shift the amplification reaction temporally and spatially. On the figure 8B , the lower layer S1 has three distinct alcoves A1, A2, A3 allowing three distinct primers to be accommodated. These three zones are located in the optical reading zone Z and make it possible to implement the principle of multiplexing. The figure 8C shows a lower state, defining five distinct zones, four alcoves A1-A4 each made in the form of a cavity and a main zone comprising a protrusion presenting a fifth alcove A5. The stratum of the chamber which is located just above defines the optical reading zone. The optical reading zone Z has a design covering the four alcoves A1-A4 so that its volume is in fluid communication with them. The fifth alcove can be outside the optical reading zone Z, as in the design of the figure 8A .

As described above each primer can be placed in a separate alcove of the chamber, in a dry form. To facilitate drying, it is advisable to take the primers in an acid buffer (approximately pH 6) and facilitate their bond with the glass of the slide. It is also possible to use sugars (eg trehalose) to limit the diffusion of the drop and potentially increase the stability of the dried DNA sequence.

• Une polyvalence qui lui permet de mettre en œuvre de manière fiable certaines étapes du procédé de préparation et d'analyse d'un échantillon biologique ou toutes les étapes de ce procédé ;
• Un dispositif facilement transportable et manipulable :
• Un dispositif monobloc, permettant de réaliser toutes les étapes dans un unique support micro-fluidique, sans transfert d'échantillon et donc sans risque de contamination ;
• Un dispositif qui présente une solution de contrôle de réaction, grâce au design particulier de sa chambre d'amplification.

It is understood from the above elements that the device of the invention has many advantages, among which:

• A versatility which allows it to reliably implement certain steps of the method for preparing and analyzing a biological sample or all the steps of this method;
• An easily transportable and manipulable device:
• A one-piece device, allowing all the steps to be carried out in a single microfluidic support, without sample transfer and therefore without risk of contamination;
• A device that presents a reaction control solution, thanks to the particular design of its amplification chamber.

Claims (11)

1. Microfluidic device for preparing and analyzing a biological sample containing biological species (4), said device comprising:

   - a single rigid support (S),

   - a first unit (U1) comprising a first chamber (10) of nonzero volume delimited by walls of the support, a filter (14) separating said first chamber (10) into a first space (101) and a second space (100), a first channel (11) made in said support opening at one end onto a surface of said support and at another end into said first space (101) and a second channel (12) made in said support and opening at one end onto a surface of said support and at another end into said second space (100),

   characterized in that the device has:

   - a second unit (U2) comprising a second chamber (20) made in said rigid support (S) and delimited at least partially by a transparent wall (200, 201) of said support (S), a third channel (21) made in said support (S) and opening at one end onto a surface of said support and at another end into said second chamber (20),

   - a first fluidic transfer channel (22) between the first chamber (10) and the second chamber (20), made in said support (S) and opening on the one hand into said second chamber (20) and on the other hand at a first bypass node in said second channel (12),

   - first flow switching means arranged for selecting connection of the first chamber:

   - to the exterior only, via the second channel only, by sealing the mouth of the first transfer channel (22) at the level of the first bypass node, or

   - to the second chamber only, through the first transfer channel, by opening the connection between the second channel (12) and the second transfer channel (22) at the level of the first bypass node.
2. Device according to Claim 1, characterized in that the first unit comprises a rough contact surface (15) made at the bottom of its first chamber (10).
3. Device according to Claim 1 or 2, characterized in that the first chamber is closed by a deformable membrane (13).
4. Device according to one of Claims 1 to 3, characterized in that it comprises a first hydrophobic membrane (210) sealing the third channel (21).
5. Device according to one of Claims 1 to 4, characterized in that it comprises:

   - a third unit (U3) comprising a third chamber (30) made in said rigid support (S) and delimited at least partially by a transparent wall (300, 301) of said support (S), a fourth channel (31) made in said support (S) and opening at one end onto a surface of said support and at another end into said third chamber (30).
6. Device according to Claim 5, characterized in that it comprises:

   - a second fluidic transfer channel (32) between the first chamber (10) and the third chamber (30), made in said support (S) and opening on the one hand into said third chamber (30) and on the other hand at a second bypass node into said first channel (11).
7. Device according to Claim 6, characterized in that it comprises second flow switching means arranged for selecting connection of the first chamber:

   - to the exterior only via the first channel only or,

   - to the third chamber only through the second transfer channel.
8. Device according to one of Claims 5 to 7, characterized in that it comprises a second hydrophobic membrane (310) sealing the fourth channel (31).
9. Device according to one of Claims 1 to 8, characterized in that the second chamber comprises at least one recess intended to receive a compound for internal reaction control.
10. Device according to Claim 9, characterized in that the second chamber is made up of several superposed strata and in that said recess is made in one of said strata only.
11. Method for preparing and analyzing a biological sample containing biological species, characterized in that it is carried out by means of a microfluidic device as defined in one of Claims 5 to 8, or as defined in either of Claims 9 and 10 when Claim 9 is dependent on one of Claims 5 to 8, and in that:

    - the first unit (U1) is configured for carrying out one or more of the following steps of said method:

    > concentrating the biological species present in a biological sample,

    > washing to purify the biological species,

    > receiving a culture medium,

    > culturing the biological species,

    > lysis of the biological species in order to release a biological material,

    > separating the biological material,

    - The second unit (U2) is configured for carrying out one or more of the following steps of said method:

    > culturing the biological species,

    > visual monitoring of growth during said culture step,

    > detecting the presence of pathogens in the separated biological material, by biomolecular amplification,

    - The third unit (U3) is configured for carrying out the following step of said method:
    > detecting the presence of pathogens in the separated biological material, by biomolecular amplification.

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